Exercise 2
{A. Use Netscape and the Web to Find and Extract a SWISS-PROT Sequence:}
{1. Turn on Netscape Communicator.}
{manuever via Hypertext links for awhile}
{2. Bioinformatics Links: the DNASYSTEM Web Page or the CMS MBR Web Page}
{a. Go to the DNASYSTEM or the CMS MBR Web Page}
{Spend a little time browsing the DNASYSTEM Web Page or the CMS MBR Web Page.}
{3. SWISS-PROT and TrEMBL at the ExPASy Web site}
{From the DNASYSTEM Web Page or from the links above, click on "General Sites'}
{Access the ExPASy site by clicking on 'ExPASy'.}
{Browse a bit to see what's at ExPASy ...}
{4. Find your Protein Sequence in the SWISS-PROT and TrEMBL Protein Databases}
{In "Access to SWISS-PROT and TrEMBL', click on "by description or identification"}
{Now enter TWO keywords in the box shown and click "Submit"}
{Try a keyword search with TWO words and record your findings; Use your own keywords; do NOT use lambda repressor ! also try REVERSING the two keywords.}
{Do the same keyword search but with each keyword separately; record your findings}
{5. Copy your Sequence}
{Choose one of the Protein Sequences you found and have a look at it by clicking on the hypertext-linked SwissProt name for the sequence.}
{Note the links present to visualize the protein and to learn more about its structural elements. Browse through some of these links.}
{Obtain a copy of the sequence entry}
{Save copies both as "Text" and "Source" from both "NiceProt View" and "old SP format"}
{Include some or all of the "Text" version of the "old SP format" in your Notebook}
{Note the First line in the Entry and the Last line in the Entry. What are these?}
{Note also the First Two Letters in each line of the "old SP format".}
{Use COPY-PASTE to COPY the Sequence directly from the Netscape window and PASTE it into your Notebook file for Exercise 1.}
{B. Searches using Boolean Operators}
{1. Go to the SWISS-PROT full text search service.}
{2. Enter the two keywords into the search box and hit SUBMIT to start the search. How many matches were reported?}
{Now reverse the order of the TWO keywords, i.e. "repressor lambda" instead of "lambda repressor."}
{Now go back to the SWISS-PROT fill text search page and try again using EACH of the two keywords. How many matches were reported?}
{Do the above searchs with the "append * before and after" option selected}
{Construct a table of your results as per the following}
{3. Do a search with the same two keywords using the AND operator. How many matches did you get? What are the results when you reverse the order of the keywords?}
{Do the same for both the OR and NOT boolean operators, and construct a table for your Notebook similar to the one below.}
{Try also parts of keywords. For example, for "lambda repressor", we would try "lam AND rep". Note that you must check the "Prefix and append wildcard '*' to words." box with this server. Try the equivalent to "lam* AND *rep*" for your keywords.}
{C. Looking up Sequences with NCBI Entrez}
{1. Go to NCBI Entrez and read some of the "Entrez Help" information.}
{2. Return to the Entrez Home page using the NetScape "Back" operation and click on "Proteins" to search for a protein sequence.}
{3. Enter one of the keywords you used at ExPASy in the search box and click the "Go" button (or just do a RETURN) to start the search.}
{4. If the number of matches is greater than 200, use a second and/or third keyword in the <keyword(s)> section together with appropriate Boolean Operators.}
{5. Click in turn on each of the four links "Limits", "Preview/Index", "History", "Clipboard". Answer the Exercise Questions on these four links. Redo the AND query with two of your keywords using "Limits" to limit your search to new GenPept entries within the past 5 years. Compare these results with those above.}
{6. In the "Display <menu>" section, choose different items from the <menu> and click the "Display" button. Briefly describe what the different items are in the <menu>, particularly the "Neighborhood" and "Link" items.}
{7. Return to the <menu> item termed "Summary" and click the "Display" button. Select the boxes of any five (5) of the sequences by clicking on each of the boxes. Select "GenPept" from the <menu> and click on the "Display" button. Record in your Lab Notebook what this has done.}
{8. The GenPept sequences are Displayed as HTML. Click on the HTML button, choose "Plain Text", and click on the "Display" button. Record in your Lab Notebook what this has done.}
{9. Examine the contents of the GenPept annotation for the first of your Sequences. What are the Fields? Save this GenPept entry to your Lab Notebook.}
{10. Return to the display of your GenPept sequences as HTML, and select from <menu> the "Graphics" option and click on the "Display" button. Describe what you see. What options does the User have? The Graphics display is only of the first of your five sequences; how would you observe the graphics for the fourth sequence?}
{11. Return to a "Display GenPept as HTML" and click on the "Add to Clipboard" button. Describe what happened.}
{12. Choose "Summary" from the <menu> and click on the "Display" button. Note the links to the far right for each of your five GenPept sequences. Briefly describe what each of these links do.}
{13. Click on "Related Sequences" for one of your five GenPept Sequences. Briefly describe what this does.}
{14. Use the Netscape Back command to return to the "Display Summary" page for the five GenPept sequences, and click on "PubMed" for the GenPept Sequence that you saved for your Lab Notebook above. How do the PubMed References that come up compare with those in the GenPept annotation for this sequence? Now click on "Related Articles" for one of these References. How does this compare with the "Related Sequences" for the GenPept Sequence itself?}
{15. Use the Netscape Back command to return to the "Display Summary" page for the five GenPept sequences, and do the same for the "Nucleotide", "Genome", and "Taxonomy" links if present. Briefly describe what each does.}
{D. Introduction to the GCG Package}
{1. Log into the GCG server machine and set up the GCG package. }
{2. Familiarize yourself with the capabilities of the GCG package. }
{3. Initialize the GCG graphics system. }
{4. Make a test plot and save it to your lab report.}
{5. Format a sequence for use with the GCGpackage.}
{6. Format a sequence using a text editor and the reformat command.}
{E. Questions:}
{Answer all of the following questions:}